rs5955415

Variant names:

• chrX-140231900-C-G
• rs5955415

Your query was ambiguous. Multiple possible variants found:

• chrX-140231900-C-G
• chrX-140231900-C-T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.146 in 111,236 control chromosomes in the GnomAD database, including 1,075 homozygotes. There are 4,587 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.15 (1075 hom., 4587 hem., cov: 23)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.546
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.25 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.146 AC: 16216 AN: 111182 Hom.: 1073 Cov.: 23

Gnomad AFR AF: 0.254

Gnomad AMI AF: 0.180

Gnomad AMR AF: 0.127

Gnomad ASJ AF: 0.174

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.0446

Gnomad FIN AF: 0.110

Gnomad MID AF: 0.123

Gnomad NFE AF: 0.105

Gnomad OTH AF: 0.130

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.146 AC: 16244 AN: 111236 Hom.: 1075 Cov.: 23 AF XY: 0.137 AC XY: 4587 AN XY: 33466

African (AFR) AF: 0.254 AC: 7755 AN: 30503

American (AMR) AF: 0.127 AC: 1326 AN: 10451

Ashkenazi Jewish (ASJ) AF: 0.174 AC: 461 AN: 2648

East Asian (EAS) AF: 0.00 AC: 0 AN: 3540

South Asian (SAS) AF: 0.0451 AC: 119 AN: 2641

European-Finnish (FIN) AF: 0.110 AC: 657 AN: 5984

Middle Eastern (MID) AF: 0.130 AC: 28 AN: 215

European-Non Finnish (NFE) AF: 0.105 AC: 5583 AN: 53067

Other (OTH) AF: 0.128 AC: 194 AN: 1516

Alfa AF: 0.0409 Hom.: 202

Bravo AF: 0.155

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.96
DANN	Benign	0.53
PhyloP100		-0.55

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs5955415; hg19: chrX-139314056;